Tag: Maximum Likelihood

GAML 0.1 – Genome Assembly by Maximum Likelihood

GAML 0.1

:: DESCRIPTION

GAML is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of indvidual sequencing technologies.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GAML

:: MORE INFORMATION

Citation

GAML: genome assembly by maximum likelihood.
Boža V, Brejová B, Vinař T.
Algorithms Mol Biol. 2015 Jun 3;10:18. doi: 10.1186/s13015-015-0052-6.

FretTrace 1.0 – Maximum Likelihood Trajectories from Single-molecule FRET Experiments

FretTrace 1.0

:: DESCRIPTION

FretTrace is the implementation of a maximum likelihood based theory. Single molecule Fluorescence Resonance Energy Transfer (FRET) experiments are a powerful and versatile tool for studying conformational motions of single biomolecules at a millisecond time scale. Typically, the small number of recorded photons limits the achieved time resolution.

::DEVELOPER

Gunnar Schröder and Helmut Grubmüller

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

  FretTrace

:: MORE INFORMATION

Citation

G. F. Schroder and H. Grubmuller,
Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments
J. Chem. Phys. 119: 9920-9924 (2003)

GARLI 2.0.1 – Phylogenetic Analysis of Molecular Sequence data using the Maximum-likelihood Criterion

GARLI 2.0.1

:: DESCRIPTION

GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned nucleotide, codon and amino acid data sets using the maximum likelihood criterion. On a practical level, the program is able to perform maximum-likelihood tree searches on large data sets in a number of hours.

::DEVELOPER

Derrick Zwickl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux

:: DOWNLOAD

 GARLI

:: MORE INFORMATION

PMLE 2.0 – Maximum Likelihood Estimation of Migration Rates for Wright Island Model

PMLE 2.0

:: DESCRIPTION

PMLE estimates the gene flow parameter q for a collection of two or more semi-isolated populations by (pseudo) maximum likelihood using either single or multi locus, haploid or diploid, genotype data. Suitable molecular data types minimally include allozymes, microsatellites, and RFLPs.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 PMLE

:: MORE INFORMATION

Citation

Rannala, B., and J. A. Hartigan. 1996.
Estimating gene flow in island populations.
Genetical Research 67:147-158

BACTFREQ – Maximum Likelihood Estimation of Bacterial Allele Frequencies

BACTFREQ

:: DESCRIPTION

BACTFREQ estimates allele frequencies and perform the Monte Carlo simulations (replaces BFREQ program)

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • C Compiler

:: DOWNLOAD

  BACTFREQ

:: MORE INFORMATION

Citation

E. C. Anderson and P. A. Scheet. 2001.
Improving the estimation of bacterial allele frequencies.
Genetics 158:1383-1386.

B. Rannala, W. Qui, and D. E. Dykhuizen. 2000.
Methods for estimating gene frequencies and detecting selection in bacterial populations
Genetics 155: 499-508.

ANCML 1.0 – Ancestor States using Maximum Likelihood

ANCML 1.0

:: DESCRIPTION

The program ANCML (Ancestor states using maximum likelihood) estimates ancestor states for a continuous trait, and provides a “standard error” for the marginal distribution of each estimate

::DEVELOPER

Dolph Schluter lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 ANCML

:: MORE INFORMATION

Citation

Schluter, D., T. Price, A. Ø. Mooers and D. Ludwig. 1998.
Likelihood of ancestor states in adaptive radiation.
Evolution 51: 1699-1711.

CodonPhyML 1.00 – Phylogeny Inference under Codon Models using Maximum Likelihood

CodonPhyML 1.00

:: DESCRIPTION

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship.

::DEVELOPER

Maria Anisimova

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CodonPhyML 

:: MORE INFORMATION

MISAT 1.0 – Microsatellite Analysis by Maximum Likelihood

MISAT 1.0

:: DESCRIPTION

MISAT is a program for estimating the likelihood surface for q (4 times the effective population size times the mutation rate) for microsatellite data. Two models are implemented: a stepwise mutation model and a mutation model allowing multi-step mutations, i.e. mutational jumps larger than on repeat unit in size.

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MISAT

:: MORE INFORMATION

Citation:

Nielsen, R. 1997.
A Maximum Likelihood Approach to Population Samples of Microsatellite alleles.
Genetics. 146: 711-716.

PHASE 2.0 – Bayesian & Maximum Likelihood Phylogenetic Inference Package

PHASE 2.0

:: DESCRIPTION

PHASE (PHylogenetics And Sequence Evolution)  is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.This package is designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. It is well known that compensatory substitutions occur in the paired regions of RNA secondary structures; this means that substitutions occurring on one side of a pair are correlated with substitutions on the other side. Most phylogenetic programs assume that each site in a molecule evolves independently of the others but this assumption is not valid for RNA genes.

::DEVELOPER

Rattray Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

PHASE

:: MORE INFORMATION

Citation

V. Gowri-Shankar and M. Rattray.
A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model” Molecular Biology and Evolution
Molecular Biology and Evolution 24(6):1286-1299 (2007).

iParameterEstimation 0.3.1 – Maximum Likelihood Parameter Estimation Package

iParameterEstimation 0.3.1

:: DESCRIPTION

iParameterEstimation is a highly configurable maximum likelihood parameter estimation package for generalized Hidden Markov Models. Specific configuration files are included for training Twinscan, N-SCAN and their EST variants.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 iParameterEstimation

:: MORE INFORMATION